Abstract: HIV-1 infection and drug of abuse have devastating effects on function of the entire organism. The macrophage is the prime member of the mononuclear phagocyte class of cells and a key part of innate immunity system. Because the macrophage is also a target of HIV, a reservoir of productive viral infection and a vehicle to spread infection to many organs, its impact on the course of disease is central. The complexity of HIV infection is further complicated and intensified by use of drugs of abuse. Methamphetamine (Meth) was chosen since it is a drug with increasing popularity among the drug-abusing population and used by those with, or at risk for HIV. Treatment of these individuals is a very complex process because it has to target two entities that are quite different in nature. As two main avenues of Systems Biology, global profiling techniques and computational processing of large data sets, mature, it becomes feasible to start analyzing data from multivariate experiments. Prior reductionist approaches precluded performing experiments at this level of complexity. Moreover, despite substantive research efforts, the broad picture of molecular mechanisms underlying functions of macrophages in the complex environment of HIV-1 infection and/or Meth use is far from being understood. Summarizing, we hypothesize that merging proteomics, metabolomics and computational analyses into a comprehensive systems biology approach to investigate regulatory mechanisms will provide unique information that will lead to the identification of new paradigms on how the MP responds to the complex environment of HIV infection and/or Meth insult. We expect that targeted profiling, computational biology, and bioinformatic analyses will uncover new and unreported mechanisms of MP regulation and will model functional networks that can be validated by focused and targeted experiments as they exist in ex vivo material from non-human primates. Better understanding of the epigenetic regulation of MP will enable us to define weak points of the major target cell under insult of viral infection and Meth. Three specific aims are proposed: 1. To characterize the networks of epigenetic factors in human monocyte derived macrophage (MDM) induced by HIV infection and/or Meth. 2. To characterize changes in intra- and extracellular metabolomes of MDM induced by HIV infection and/or Meth treatment resulting from alterations in regulatory functions of transcription factors and regulators (TF&R) and 3. To validate integrated complex proteomic and metabolomic data in ex vivo human samples to build new paradigms of how HIV and/or Meth regulate the MP.